A wet lab for AI-ready spatial biology datasets in oncology
Explicyte generates production-scale spatial transcriptomics, single-cell, and digital pathology datasets from human tissues sourced through accredited biobanks.
We deliver in open formats, ready for ingestion into your AI pipeline.
Supporting biology foundation models
Dataset generation, controlled end-to-end
Cohort Design & Sourcing
Unique cohorts and ready-to-use data, sourced for you
- Cohort design with PhD-level expertise — indications, controls, stratification, sample size for statistical power
- Multiple sample types — tumor and normal FFPE tissues, blood-derived samples
- Sample sourcing through regulatory-compliant biobanks
- De-identified metadata — clinical, histopathological and epidemiological, subject to project-specific availability and permitted use
Sample QC & processing
Wet lab rigor to process the right samples & minimize batch effects
- Quality-managed sample handling and ISO-certified digital pathology workflows
- QC on every sample — RNA quality assessment (RNAscope), histopathological review by expert pathologists
- Scalable processing capacity — standardized sectioning, batch controls, and pre-analytical workflows that minimize variability across cohorts
Data Generation & Delivery
Fast, cost-efficient data generation, AI-ready delivery
- Production capacity built for speed — redundant on-site platforms (2× Xenium, 2× Ventana, 2× PhenoImager) enable parallel runs and fast turnaround
- Cost-optimization strategies — sample multiplexing, fit-for-purpose panel design, and tiered service options to match your budget
- Open-format datasets — OME-TIFF, AnnData, H5 — delivered via secure high-speed transfer, structured for downstream ingestion
- Optional data cleaning and normalization — kickstart your analysis with pre-processed datasets
Our production platforms
Scalable platforms for multimodal AI-ready dataset generation
Spatial transcriptomics
Atera
High-throughput whole-transcriptome spatial profiling with single-cell sensitivity
Explore platform
Spatial transcriptomics
Xenium (×2)
Single-cell spatial transcriptomics with
5K or 300-500-plex focused panels
Explore platform
Spatial transcriptomics
Visium HD
Whole-transcriptome mapping at high resolution, co-registration to H&E or IF
Explore platform
Digital pathology
PhenoImager HT (×2)
Singleplex IHC and multiplex IF panels for protein-level target validation
Explore platform
Spatial transcriptomics
GeoMx
Whole transcriptome spatial profiling for compartment-level questions
Explore platform
Single-cell RNA-seq
Chromium X
High-throughput single-cell gene expression profiling for large-scale cellular datasets
Explore platform
Paul Marteau, PharmD (study director), Imane Nafia, PhD (CSO), Loïc Cerf, MSc (COO), Alban Bessede, PhD (founder, CEO), Jean-Philippe Guégan, PhD (CTO)
Contact our team
Discuss your AI dataset project
Whether you're training a foundation model, benchmarking a new approach, or building a validation cohort, we can scope the right dataset and propose next steps. Within 3 business days, a PhD-level scientist will reach out to discuss your project, propose the right cohort and dataset strategy, and provide pricing.
Frequently asked questions
Frequently asked questions about AI-ready spatial biology datasets
What is AI-ready spatial biology data?
AI-ready spatial biology data refers to large-scale, structured datasets generated from human tissues — combining spatial transcriptomics, single-cell, or digital pathology readouts with clinical and pathological metadata — designed to be ingested directly into machine learning pipelines. Three properties matter most: consistent generation under quality-controlled conditions (to minimize batch effects), open-format delivery with documented schemas (to avoid preprocessing overhead), and verifiable provenance (to meet consent and regulatory requirements for AI training data). Explicyte generates AI-ready datasets across Atera, Xenium, Visium HD, Chromium X, IHC and multiplex IF.
Can you support large-scale dataset generation?
Capacity depends on platform and panel design. With two on-site Xeniums, two Ventana stainers, and two PhenoImager scanners running in parallel, we can sustain production-scale throughput across cohorts of hundreds to thousands of samples. Typical project timelines range from a few weeks for focused panels on small cohorts to a few months for large multi-modality datasets. We confirm capacity and turnaround during project scoping based on your specific dataset specifications.
In what format do you deliver data?
Datasets are delivered in open, AI-pipeline-compatible formats: OME-TIFF for imaging data (digital pathology, multiplex IF, Xenium), AnnData and H5 for single-cell and spatial transcriptomic data, and standard tabular formats (CSV, Parquet) for metadata and tabular results. Every dataset comes with full documentation — schema descriptions, data dictionaries, QC metrics, and methodology notes — to enable direct ingestion into your machine learning workflows. Custom formats can be accommodated on request.
Can we use Explicyte-generated data for AI model training?
Yes, where the project-specific sourcing framework and agreed data-use rights permit the intended AI application. We document sample provenance, applicable consent or non-opposition frameworks, de-identification, processing and data lineage. Specific training rights, exclusivity and downstream usage permissions are defined during project scoping and contracting.
How do you ensure ethical sourcing and consent for AI applications?
All human tissues are sourced through partnerships with regulatory-compliant biobanks. Samples are sourced under the applicable consent or non-opposition framework through our biobank partners; data reaches Explicyte fully de-identified. Chain-of-custody and data-provenance documentation are maintained throughout the project to support sponsor due diligence, data governance and applicable regulatory requirements.
What makes Explicyte different from other dataset providers for AI?
Three things. First, we’re a wet lab partner, not a biospecimen vendor — sourcing, processing, and dataset generation happen end-to-end under one study director, so AI teams don’t need to coordinate across multiple suppliers. Second, redundant on-site platforms enable parallel processing, capacity planning and continuity for large dataset-generation programs. Third, we deliver in open formats (OME-TIFF, AnnData, H5) with documentation built for AI ingestion — proven through partnerships with foundation model developers and clinical research teams. ISO-certified digital pathology workflows and 10x Genomics Certified Service Provider status anchor the regulatory credibility.
Can you generate proprietary datasets for our exclusive use?
Do you support foundation model training data needs?
Yes. Foundation model training requires datasets at production scale, with consistent generation conditions and clean, documented metadata — exactly what our redundant on-site platforms and ISO-certified workflows are built to deliver. We’ve supported foundation model partners through cohort design, sample sourcing under accredited biobank frameworks, multi-modality data generation (spatial transcriptomics + digital pathology), and dataset delivery in AI-pipeline-compatible formats.
Do you provide bioinformatics preprocessing, or just raw data?
Can you integrate with our data pipeline / cloud infrastructure?
Datasets are delivered via secure high-speed transfer in formats compatible with common cloud and on-premise infrastructure (AWS, GCP, Azure, on-prem clusters). For sponsors with specific pipeline requirements — direct cloud bucket delivery, custom schema mapping, or dataset versioning protocols — we can adapt delivery workflows during scoping. We do not require sponsors to use Explicyte-specific infrastructure or proprietary file formats at any stage.
